Boa Morte has already served a one match ban after being found guilty of improper conduct for an incident involving Frank Sinclair during the game with Leicester earlier this season.
The FA this time are charging the Portugese international striker for an incident involving the crowd at Loftus Road.
"Boa Morte has been charged for improper conduct under rule E1. The charge relates to an incident involving the player and supporters," a statement on the FA's official website reads.